All MySQL databases disappeared on my server - recovered one website but not others

mandywhite

Registered
Sep 18, 2013
1
0
1
cPanel Access Level
Website Owner
I have 2 websites on my server on 2 different IP addresses. I have managed to bring back the first by adding:

open_files_limit = 200000

via SSH.

I added the same to the second website but it made no difference. When I go into cpanel MySQLDatabases, there are no websites or users, but when I try to re-add the database name it comes back with an error saying the database already exists.

When I go into phpmyadmin, the database names are there, but when I click on any of them I get the following message:

Error
SQL query: DocumentationEdit Edit

SELECT *
FROM data_dictionary.CHARACTER_SETS

MySQL said: Documentation

#1142 - SELECT command denied to user 'mysite'@'localhost' for table 'CHARACTER_SETS'

I then followed the suggestions in another thread on here and ran the following commands in SSH (one after the other):

/scripts/upcp/ ~~force
/scripts/checkperlmodules ~~force
/usr/local/cpanel/bin/setupdbmap

and this is the result:

Code:
[20130919.113942]      [10456] Sep 19 11:39:42.972 [10457] dbg: channel: adding 73_sandbox_manual_scores.cf
[20130919.113942]      [10456] Sep 19 11:39:42.973 [10457] dbg: channel: adding local.cf
[20130919.113942]      [10456] Sep 19 11:39:42.973 [10457] dbg: channel: adding regression_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.973 [10457] dbg: channel: update complete
[20130919.113942]      [10456] Sep 19 11:39:42.973 [10457] dbg: generic: cleaning up temporary directory/files
[20130919.113942]      [10456] Sep 19 11:39:42.974 [10457] dbg: generic: unlinking 20_dynrdns.cf
[20130919.113942]      [10456] Sep 19 11:39:42.974 [10457] dbg: generic: unlinking 20_head_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.974 [10457] dbg: generic: unlinking 20_fake_helo_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.974 [10457] dbg: generic: unlinking 72_active.cf
[20130919.113942]      [10456] Sep 19 11:39:42.975 [10457] dbg: generic: unlinking 25_textcat.cf
[20130919.113942]      [10456] Sep 19 11:39:42.975 [10457] dbg: generic: unlinking 60_adsp_override_dkim.cf
[20130919.113942]      [10456] Sep 19 11:39:42.975 [10457] dbg: generic: unlinking 30_text_it.cf
[20130919.113942]      [10456] Sep 19 11:39:42.975 [10457] dbg: generic: unlinking 25_spf.cf
[20130919.113942]      [10456] Sep 19 11:39:42.976 [10457] dbg: generic: unlinking 20_ratware.cf
[20130919.113942]      [10456] Sep 19 11:39:42.976 [10457] dbg: generic: unlinking sa-update-pubkey.txt
[20130919.113942]      [10456] Sep 19 11:39:42.976 [10457] dbg: generic: unlinking 20_freemail_domains.cf
[20130919.113942]      [10456] Sep 19 11:39:42.976 [10457] dbg: generic: unlinking 30_text_de.cf
[20130919.113942]      [10456] Sep 19 11:39:42.977 [10457] dbg: generic: unlinking 25_accessdb.cf
[20130919.113942]      [10456] Sep 19 11:39:42.977 [10457] dbg: generic: unlinking 25_asn.cf
[20130919.113942]      [10456] Sep 19 11:39:42.977 [10457] dbg: generic: unlinking 25_dkim.cf
[20130919.113942]      [10456] Sep 19 11:39:42.977 [10457] dbg: generic: unlinking 50_scores.cf
[20130919.113942]      [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking 20_drugs.cf
[20130919.113942]      [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking 20_advance_fee.cf
[20130919.113942]      [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking local.cf
[20130919.113942]      [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking user_prefs.template
[20130919.113942]      [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking 73_sandbox_manual_scores.cf
[20130919.113942]      [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 10_hasbase.cf
[20130919.113942]      [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 25_uribl.cf
[20130919.113942]      [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 20_net_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 25_hashcash.cf
[20130919.113942]      [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 23_bayes.cf
[20130919.113942]      [10456] Sep 19 11:39:42.980 [10457] dbg: generic: unlinking 20_compensate.cf
[20130919.113942]      [10456] Sep 19 11:39:42.980 [10457] dbg: generic: unlinking 20_porn.cf
[20130919.113942]      [10456] Sep 19 11:39:42.980 [10457] dbg: generic: unlinking 20_uri_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.980 [10457] dbg: generic: unlinking 20_mailspike.cf
[20130919.113942]      [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 20_aux_tlds.cf
[20130919.113942]      [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 72_scores.cf
[20130919.113942]      [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 20_freemail.cf
[20130919.113942]      [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 25_pyzor.cf
[20130919.113942]      [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 60_whitelist_subject.cf
[20130919.113942]      [10456] Sep 19 11:39:42.982 [10457] dbg: generic: unlinking STATISTICS-set0-72_scores.cf.txt
[20130919.113942]      [10456] Sep 19 11:39:42.982 [10457] dbg: generic: unlinking 25_antivirus.cf
[20130919.113942]      [10456] Sep 19 11:39:42.982 [10457] dbg: generic: unlinking 30_text_fr.cf
[20130919.113942]      [10456] Sep 19 11:39:42.982 [10457] dbg: generic: unlinking STATISTICS-set1-72_scores.cf.txt
[20130919.113942]      [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking 60_whitelist_spf.cf
[20130919.113942]      [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking 20_vbounce.cf
[20130919.113942]      [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking STATISTICS-set3-72_scores.cf.txt
[20130919.113942]      [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking 20_imageinfo.cf
[20130919.113942]      [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking 20_phrases.cf
[20130919.113942]      [10456] Sep 19 11:39:42.984 [10457] dbg: generic: unlinking 20_html_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.984 [10457] dbg: generic: unlinking 25_razor2.cf
[20130919.113942]      [10456] Sep 19 11:39:42.984 [10457] dbg: generic: unlinking 30_text_pt_br.cf
[20130919.113942]      [10456] Sep 19 11:39:42.984 [10457] dbg: generic: unlinking regression_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.985 [10457] dbg: generic: unlinking 10_default_prefs.cf
[20130919.113942]      [10456] Sep 19 11:39:42.985 [10457] dbg: generic: unlinking languages
[20130919.113942]      [10456] Sep 19 11:39:42.985 [10457] dbg: generic: unlinking 60_shortcircuit.cf
[20130919.113942]      [10456] Sep 19 11:39:42.985 [10457] dbg: generic: unlinking 20_meta_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 20_dnsbl_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 60_awl.cf
[20130919.113942]      [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 30_text_nl.cf
[20130919.113942]      [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 60_whitelist_dkim.cf
[20130919.113942]      [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 30_text_pl.cf
[20130919.113942]      [10456] Sep 19 11:39:42.987 [10457] dbg: generic: unlinking STATISTICS-set2-72_scores.cf.txt
[20130919.113942]      [10456] Sep 19 11:39:42.987 [10457] dbg: generic: unlinking 20_body_tests.cf
[20130919.113942]      [10456] Sep 19 11:39:42.987 [10457] dbg: generic: unlinking 25_dcc.cf
[20130919.113942]      [10456] Sep 19 11:39:42.987 [10457] dbg: generic: unlinking 60_whitelist.cf
[20130919.113942]      [10456] Sep 19 11:39:42.988 [10457] dbg: generic: unlinking 25_replace.cf
[20130919.113942]      [10456] Sep 19 11:39:42.988 [10457] dbg: diag: updates complete, exiting with code 0
[20130919.113943]      [10456] Done
[20130919.113945]      [10456] Checking update....update ok!
[20130919.113945]   Processing: Restoring compiler permissions
[20130919.113945]    - Processing command `/usr/local/cpanel/scripts/compilers restore`
[20130919.113945]      [10460] Compilers are enabled for unprivileged users.
[20130919.113945]   Processing: Cleaning SpamAssassin DBM files
[20130919.113945]    - Processing command `/usr/local/cpanel/scripts/spamassassin_dbm_cleaner`
[20130919.113945]      [10461] /usr/local/cpanel/scripts/spamassassin_dbm_cleaner: version 1.0
[20130919.113945]      [10461] Checking SpamAssassin dbm databases....Done
[20130919.113945]      [10461] Checked 0 files for  user(s),  ok,  broken
[20130919.113945]   Processing: Configuring Frontpage
[20130919.113945]    - Processing command `/usr/local/cpanel/scripts/initfpsuexec`
[20130919.113945]      [10462] initfpsuexec: using apache 1.x support
[20130919.113945]      [10462] chattr: No such file or directory while trying to stat _vti_bin/fpexe
[20130919.113945]      [10462] grep: /usr/local/frontpage/version5.0/apache-fp/_vti_bin/fpexe: No such file or directory
[20130919.113945]      [10462] x - creating lock directory
[20130919.113945]      [10462] x - extracting /usr/local/frontpage/version5.0/apache-fp/fpexe.c (text)
[20130919.113945]      [10462] x - creating lock directory
[20130919.113945]      [10462] x - extracting /usr/local/frontpage/version5.0/apache-fp/fpexe2.patch (text)
[20130919.113945]      [10462] patching file fpexe.c
[20130919.113945]      [10462] C compiler (/usr/bin/gcc) OK (cached Thu Sep 19 03:58:38 2013)
[20130919.113945]      [10462] Tuned C compiler not available because it is not enabled
[20130919.113945]      [10462] Using Frontpage with suexec
[20130919.113945]      [10462] /usr/bin/ld: cannot open output file _vti_bin/fpexe: No such file or directory
[20130919.113945]      [10462] collect2: ld returned 1 exit status
[20130919.113945]      [10462] chown: cannot access `_vti_bin': No such file or directory
[20130919.113945]      [10462] chmod: cannot access `_vti_bin/fpexe': No such file or directory
[20130919.113945]      [10462] chattr: No such file or directory while trying to stat _vti_bin/fpexe
[20130919.113945]   Cleaning Squirrelmail attachment directories
[20130919.113945]   Processing: Running former postinstall scripts
[20130919.113945]    - Processing command `/usr/local/cpanel/bin/dcpumon --killproc`
[20130919.113945]      [10557] Added Contact [email protected]
[20130919.113945]    - Processing command `/usr/local/cpanel/bin/scanfornewmail`
[20130919.113945]      [10560] Scanning for new mail senders.....Done
[20130919.113945]    - Processing command `/usr/local/cpanel/scripts/fixsuexeccgiscripts`
[20130919.113945]      [10561] Scanning suexec_log...Done
[20130919.113945]    - Processing command `/usr/local/cpanel/bin/setupdbmap`
[20130919.113946]    - Processing command `/usr/local/cpanel/bin/fix_userdata_perms`
[20130919.113946]    - Processing command `/usr/local/cpanel/scripts/detect_env_capabilities`
[20130919.113946]
[20130919.113946] Maintenance complete.
=> Log closed Thu Sep 19 11:39:46 2013
----------------------------------------------------------------------------------------------------
=> Log opened from cPanel Update (upcp) - Slave at Thu Sep 19 11:39:46 2013
[20130919.113946]   Maintenance completed successfully
[20130919.113946]   Running Standardized hooks
[20130919.113946]
[20130919.113946]       cPanel update completed
[20130919.113946]   A log of this update is available at /var/cpanel/updatelogs/update.1379587138.log
[20130919.113946]   Removing upcp pidfile
[20130919.113946]
[20130919.113946] Completed all updates
=> Log closed Thu Sep 19 11:39:46 2013
[email protected] [~]# /scripts/checkperlmodules ~~force
scripts/checkperlmodules is deprecated. cPanel no longer uses /usr/bin/perl and provides its perl modules as a set of RPMs. For more information, see http://go.cpanel.net/1136checkperlmodules
[email protected] [~]# /usr/local/cpanel/bin/setupdbmap
info [setupdbmap] Begin setupdbmap
info [setupdbmap] Updating MySQL users
info [setupdbmap] Processing MySQL databases and database users ...
info [setupdbmap] Finished with MySQL users
info [setupdbmap] PostgreSQL is not installed. Could not locate executable psql client.
info [setupdbmap] End setupdbmap
info [setupdbmap] Storing Database Index
info [setupdbmap] Database Index Complete
[email protected] [~]#
I reaceched mysql databases - still same issue, and rechecked phpmyadmin - also still same.

I then tried to a reinstall of my entire site using akeeba backup, but ran into problems again - when I tried to run kickstart (in the same way as I have hundreds of times before) I now get this error:

Not Found

The requested URL /kickstart.php was not found on this server.

Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.

So I appear to be stumped - I can't repair my databases and I can't re-install my site. Its like my cPanel has become corrupted if this is possible.

Can you help me?

Kind regards

Mandy
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,880
2,261
463
Hello :)

Please check the cPanel error log when accessing the "MySQL Databases" option in cPanel. The cPanel error log is located at:

Code:
/usr/local/cpanel/logs/error_log
Is there any specific output when accessing this option in cPanel?

Thank you.